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Illegitimacy and sibship assignments in oil palm (Elaeis guineensis Jacq.) half-sib families using single locus DNA microsatellite markers

Hama-Ali EO, Alwee SS, Tan SG, Panandam JM, Ling HC, Namasivayam P, et al.

Mol Biol Rep, 2015 May;42(5):917-25.
PMID: 25399079 DOI: 10.1007/s11033-014-3829-7

Oil palm breeding has been progressing very well in Southeast Asia, especially in Malaysia and Indonesia. Despite this progress, there are still problems due to the difficulty of controlled crossing in oil palm. Contaminated/illegitimate progeny has appeared in some breeding programs; late and failure of detection by the traditional method causes a waste of time and labor. The use of molecular markers improves the integrity of breeding programs in perennial crops such as oil palm. Four half-sib families with a total of 200 progeny were used in this study. Thirty polymorphic single locus DNA microsatellites markers were typed to identify the illegitimate individuals and to obtain the correct parental and progeny assignments by using the CERVUS and COLONY programs. Three illegitimate palms (1.5%) were found, and 16 loci proved to be sufficient for sibship assignments without parental genotypes by using the COLONY program. The pairwise-likelihood score (PLS) method was better for half-sib family assignments than the full likelihood (FL) method.

Matched MeSH terms: Plant Breeding/methods*
Fulltext Major QTLs for Trunk Height and Correlated Agronomic Traits Provide Insights into Multiple Trait Integration in Oil Palm Breeding

Teh CK, Ong AL, Mayes S, Massawe F, Appleton DR

Genes (Basel), 2020 07 21;11(7).
PMID: 32708151 DOI: 10.3390/genes11070826

Superior oil yield is always the top priority of the oil palm industry. Short trunk height (THT) and compactness traits have become increasingly important to improve harvesting efficiency since the industry started to suffer yield losses due to labor shortages. Breeding populations with low THT and short frond length (FL) are actually available, such as Dumpy AVROS pisifera (DAV) and Gunung Melayu dura (GM). However, multiple trait stacking still remains a challenge for oil palm breeding, which usually requires 12-20 years to complete a breeding cycle. In this study, yield and height increment in the GM × GM (GM-3341) and the GM × DAV (GM-DAV-3461) crossing programs were evaluated and palms with good yield and smaller height increment were identified. In the GM-3341 family, non-linear THT growth between THT_2008 (seven years old) and THT_2014 (13 years old) was revealed by a moderate correlation, suggesting that inter-palm competition becomes increasingly important. In total, 19 quantitative trait loci (QTLs) for THT_2008 (8), oil per palm (O/P) (7) and FL (4) were localized on the GM-3341 linkage map, with an average mapping interval of 2.01 cM. Three major QTLs for THT_2008, O/P and FL are co-located on chromosome 11 and reflect the correlation of THT_2008 with O/P and FL. Multiple trait selection for high O/P and low THT (based on the cumulative effects of positive alleles per trait) identified one palm from 100 palms, but with a large starting population of 1000-1500 seedling per cross, this low frequency could be easily compensated for during breeding selection.

Matched MeSH terms: Plant Breeding/methods*
Rapid and targeted introgression of fgr gene through marker-assisted backcrossing in rice (Oryza sativa L.)

Cheng A, Ismail I, Osman M, Hashim H, Mohd Zainual NS

Genome, 2017 Dec;60(12):1045-1050.
PMID: 28813631 DOI: 10.1139/gen-2017-0100

While it is crucial for developing countries like Malaysia to achieve self-sufficiency in rice (Oryza sativa L.), it is equally critical to be able to produce high-quality rice, specifically fragrant rice, which demands are often met through importation. The present study was aimed at developing high-yielding fragrant rice, in a timely and cost-effective manner. A marker-assisted backcross (MABC) approach was optimised to introgress the fragrance gene (fgr) into two high-yielding Malaysian varieties, MR84 and MR219, within two years utilising less than 50 molecular markers. Coupled with phenotypic screening, one single foreground marker (fgr-SNP) and 48 background markers were selected and utilised, revealing recovery of at least 90% of recurrent parent genome (RPG) in merely two backcross generations. Collectively, the yield potential of the developed BC2F2 lines (BLs) was higher (P > 0.05) than the donor parent, MRQ74, and similar (P < 0.05) to both the recurrent parents, MR84 and MR219. In addition, some of the developed BLs showed good grain quality, such as having long grain. We believe that this is the first report comprising the validation and utilisation of the single functional marker system (fgr-SNP) in introgressing the fgr gene into different rice varieties.

Matched MeSH terms: Plant Breeding/methods*
Fulltext Ageing Effects, Generation Means, and Path Coefficient Analyses on High Kernel Elongation in Mahsuri Mutan and Basmati 370 Rice Populations

Ab Halim AAB, Rafii MY, Osman MB, Oladosu Y, Chukwu SC

Biomed Res Int, 2021;2021:8350136.
PMID: 34095311 DOI: 10.1155/2021/8350136

High kernel elongation (HKE) is one of the high-quality characteristics in rice. The objectives of this study were to determine the effects of ageing treatments, gene actions, and inheritance pattern of kernel elongation on cooking quality in two populations of rice and determine the path of influence and contribution of other traits to kernel elongation in rice. Two rice populations derived from crosses between MR219 × Mahsuri Mutan and MR219 × Basmati 370 were used. The breeding materials included two F1 progenies from the two populations, and their respective parents were grown in four different batches at a week interval to synchronize the flowering between the female and male plants. Scaling tests and generation means analysis were carried out to determine ageing effects and estimate additive-dominance gene action and epistasis. The estimation of gene interaction was based on quantitative traits. Path coefficient analysis was done using SAS software version 9.4 to determine the path of influence (direct or indirect) of six quantitative traits on HKE. Results obtained showed that nonallelic gene interaction was observed in all traits. The results before ageing and after ageing showed significant differences in all traits, while the gene interaction changed after ageing. The HKE value improved after ageing, suggesting that ageing is an external factor that could influence gene expression. The epistasis effect for HKE obtained from the cross Mahsuri Mutan × MR219 showed duplicate epistasis while that obtained from a cross between Basmati 370 × MR219 showed complimentary epistasis. Besides, the heritability of HKE was higher in Basmati 370 × MR219 compared to that obtained in Mahsuri Mutan × MR219. The path analysis showed that the cooked grain length and length-width ratio positively significantly affected HKE. It was concluded that ageing treatment is an external factor that could improve the expression of HKE. The findings from this study would be useful to breeders in the selection and development of new specialty (HKE) rice varieties.

Matched MeSH terms: Plant Breeding/methods
Fulltext Evaluation of methods and marker Systems in Genomic Selection of oil palm (Elaeis guineensis Jacq.)

Kwong QB, Teh CK, Ong AL, Chew FT, Mayes S, Kulaveerasingam H, et al.

BMC Genet, 2017 Dec 11;18(1):107.
PMID: 29228905 DOI: 10.1186/s12863-017-0576-5

BACKGROUND: Genomic selection (GS) uses genome-wide markers as an attempt to accelerate genetic gain in breeding programs of both animals and plants. This approach is particularly useful for perennial crops such as oil palm, which have long breeding cycles, and for which the optimal method for GS is still under debate. In this study, we evaluated the effect of different marker systems and modeling methods for implementing GS in an introgressed dura family derived from a Deli dura x Nigerian dura (Deli x Nigerian) with 112 individuals. This family is an important breeding source for developing new mother palms for superior oil yield and bunch characters. The traits of interest selected for this study were fruit-to-bunch (F/B), shell-to-fruit (S/F), kernel-to-fruit (K/F), mesocarp-to-fruit (M/F), oil per palm (O/P) and oil-to-dry mesocarp (O/DM). The marker systems evaluated were simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). RR-BLUP, Bayesian A, B, Cπ, LASSO, Ridge Regression and two machine learning methods (SVM and Random Forest) were used to evaluate GS accuracy of the traits.
RESULTS: The kinship coefficient between individuals in this family ranged from 0.35 to 0.62. S/F and O/DM had the highest genomic heritability, whereas F/B and O/P had the lowest. The accuracies using 135 SSRs were low, with accuracies of the traits around 0.20. The average accuracy of machine learning methods was 0.24, as compared to 0.20 achieved by other methods. The trait with the highest mean accuracy was F/B (0.28), while the lowest were both M/F and O/P (0.18). By using whole genomic SNPs, the accuracies for all traits, especially for O/DM (0.43), S/F (0.39) and M/F (0.30) were improved. The average accuracy of machine learning methods was 0.32, compared to 0.31 achieved by other methods.
CONCLUSION: Due to high genomic resolution, the use of whole-genome SNPs improved the efficiency of GS dramatically for oil palm and is recommended for dura breeding programs. Machine learning slightly outperformed other methods, but required parameters optimization for GS implementation.

Matched MeSH terms: Plant Breeding/methods*
Fulltext Genetic analysis and selection of Bambara groundnut (Vigna subterranea [L.] Verdc.) landraces for high yield revealed by qualitative and quantitative traits

Khan MMH, Rafii MY, Ramlee SI, Jusoh M, Al Mamun M

Sci Rep, 2021 Apr 07;11(1):7597.
PMID: 33828137 DOI: 10.1038/s41598-021-87039-8

As a crop for the new millennium Bambara groundnut (Vigna subterranea [L.] Verdc.) considered as leading legumes in the tropical regions due to its versatile advantages. The main intent of this study was to find out the high yielding potential genotypes and considering these genotypes to develop pure lines for commercial cultivation in Malaysia. Considering the 14 qualitative and 27 quantitative traits of fifteen landraces the variation and genetic parameters namely, variability, heritability, genetic advance, characters association, and cluster matrix were determined. ANOVA revealed significant variation for all the agronomic traits (except plant height). Among the accessions, highly significant differences (P ≤ 0.01) were found for almost all the traits excluding fifty percent flowering date, seed length, seed width. The 16 traits out of the 27 quantitative traits had a coefficient of variation (CV) ≥ 20%. A positive and intermediate to perfect highly significant association (r = 0.23 to 1.00; P plant (g) had the highest GCV = 59.91% and PCV = 59.57% whereas the trait fresh pod weight (99.55%), dry seed weight (98.86%), and yield (98.10%) were highly heritable. The genetic advance recorded the highest for dry seed weight (122.01%) and lowest (3.97%) for plant height. To validate the genetic disparity, an unweighted pair-group produce with arithmetic mean (UPGMA), principal component analysis (PCA), heatmap, and H'-index was performed considering 27 quantitative traits. The constructed dendrogram showed five distinct groups of accessions. Genotypes G2, G3, and G9 from Group IV consider as promising lines which gave 70.05% higher mean yield compared to grand mean yield (1180 kg ha-1) with desirable traits. Group II had a maximum number of accessions while group III and group V had one of each. However, findings declared that the availability of genetic variance will be beneficial for this crop improvement through cross breeding as well as the plant breeders to prefer desirable traits in V. subterranea L. Verdc. for further breeding purposes.

Matched MeSH terms: Plant Breeding/methods*